News|Articles|January 12, 2026

As flu cases surge, new vaccine guidance fuels more concern

Author(s)Ron Southwick

Hospitals are seeing more patients with the flu, even as the government’s revised childhood vaccine schedule no longer recommends flu shots for all children.

The federal government’s changes to the recommended childhood vaccine schedule alarmed doctors and medical societies, but some are especially baffled at the timing.

The Health Department has trimmed the number of recommended vaccines for children, and notably dropped guidance that all children should get the influenza vaccines. Healthcare leaders have widely criticized the changes under Health Secretary Robert F. Kennedy Jr., a longtime vaccine skeptic. The American Academy of Pediatrics is keeping its vaccine recommendations intact, including the flu shot.

But critics say the changing guidance still is likely to cause more confusion, and some say the timing is particularly poor.

More than 40 states are reporting high levels of flu activity, according to the federal government’s own data (from the Centers for Disease Control and Prevention). Outpatient visits for respiratory illnesses or flu-like visits reached the highest level since at least 1997-98, according to CDC data.

Matthew Cook, CEO of the Children’s Hospital Association, tells Chief Healthcare Executive® that the changing guidance is disappointing, particularly as flu cases have surged nationwide. Federal data suggests this flu season could match the “brutal” flu seasons of the past few years, he says.

“I think that's the part that seems odd to me,” Cook says. “We're having another very significant flu season, and the recommendation changed in terms of the flu.”

(See part of our conversation in this video. The story continues below.)

‘A lot of kids’ in ED

Children’s hospitals across the country are seeing more cases of the flu, Cook says.

“All of the members I've talked to have said they have pretty high volumes related to flu,” Cook says.

“What we're seeing is a lot of kids visiting the ED and potentially being admitted,” he says.

The spike in flu cases creates capacity challenges for pediatric hospitals, and Cook says it’s especially frustrating to see higher volumes of patients because some kids aren’t getting the flu vaccine.

“I think the challenge that that creates, when we do have a vaccine that kind of mitigates the severity of illness and we're not using it, then we do have more kids show up in the emergency room and in the hospital,” Cook says. “And what that does is it takes up a bed, potentially for a child with a chronic, complex condition that might need to be admitted.”

“And so that's the concern that we have, is that when we see these dips in vaccination rates, we're concerned about what that does in terms of hospital bed availability, workforce availability and the unintended consequences of that,” he says.

Sean T. O’Leary, MD, chairman of the American Academy of Pediatrics’ Committee on Infectious Diseases, criticized the change in federal guidance and the timing in a media call.

“To back off on a flu recommendation in the midst of a pretty severe flu year seems to me to be pretty tone deaf,” O’Leary said.

In Boston, city officials reported two deaths associated with the flu in children under the age of 2. They mark the first pediatric deaths tied to the flu in Boston since 2013.

Dr. Bisola Ojikutu, Boston’s commissioner of public health, urged parents to get their children vaccinated as soon as possible.

“Flu cases are surging in Boston, and we are seeing an uptick in serious cases involving children, including the tragic deaths of two very young children,” Ojikutu said in a news release.

New York reported the highest number of flu cases in a single week in more than two decades, state officials said.

"We are having a more severe flu season than prior years, almost 1,000 more people were admitted to a hospital during this most recent 7-day period compared to the prior week," New York State Health Commissioner Dr. James McDonald said Jan. 2.

‘Messaging is really important’

The majority of children in the U.S. haven’t received a flu vaccine this year. Through Jan. 9, only 42.5% of children - and 44% of adults - have received the influenza vaccine, the CDC says.

Flu vaccination rates have plunged in recent years. In 2019, nearly two-thirds of children (63.7%) received the flu vaccine, according to CDC data.

“The flu vaccination rate has been dipping the last few years,” Cook says. “We are fairly well below the pre-pandemic flu vaccination rates.”

Read more: Family doctors face more vaccine confusion

In an interview with CBS News, Kennedy was asked about the prospect of fewer kids getting the flu vaccines in light of the new federal guidance. Kennedy responded, “Maybe that's a better thing.” He also said flu shots remain available to those who want them, but the guidance calls for consulting doctors.

Healthcare leaders say they are troubled by the revisions to the federal vaccine schedule because they occurred with little scientific review. In December, President Trump directed the health department to review the childhood vaccine schedule with schedules in other countries. Within a month, the health department announced a new, slimmer schedule.

Cook says in the past, scientists and physicians “thoroughly vetted” potential changes to the childhood vaccine recommendations.

“Experts have weighed in on it, there's been public commentary,” Cook says of past changes. “And that's not what happened in this particular change that just occurred.

“And I think that is what is frustrating for the members, is that although the recommendations have changed, the scientific evidence has not. And the safety of these vaccines is still there. It's still proven. And so I think what frustrates the members is when there are changes that's not based on the scientific evidence,” he says.

The federal vaccine schedule is not a mandate. Parents can still get their kids the vaccines they want, and states are able to maintain their own vaccine schedules.

“Even though the changes in the recommendations of the vaccine panel are at the federal level, they haven't changed at the state level,” Cook says.

The Health Department also changed its guidance for respiratory syncytial virus (RSV), meningococcal disease, hepatitis A and hepatitis B. Instead of broadly recommending those vaccines, the Health Department now recommends them only to high-risk groups.

Federal officials say all childhood vaccines will continue to be covered by insurance, regardless of whether they are recommended for all kids or not.

Cook says that parents need to get that information, and that’s a message that needs to be repeated. Physicians and medical societies have said the new guidance only adds to confusion at a time when vaccine hesitancy and misinformation are rising.

“This is the time when parents should have conversations with their pediatrician about vaccinations and what works best for them and their family,” Cook says.

“But the messaging is really important,” he continues. “Number one, these vaccines are safe and effective. That has not changed. The science has not changed around these vaccines. And at this point, parents need to understand that, and need to know that they have access to them for their children. Because what we do know is vaccines are the most effective way to prevent these illnesses.”


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